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Microarray data

There is a suite of procedures for the design, analysis and visualization of two-colour and Affymetrix microarray data. These are used by the Microarray menus in Genstat for Windows.

    AGBIB generates balanced incomplete block designs
    AGLOOP generates loop designs e.g. for time-course microarray experiments
    AGREFERENCE generates reference-level designs e.g. for microarray experiments
    BAFFYMETRIX Estimates expression values from an Affymetrix CED and CDF file
    MADESIGN assesses the efficiency of a two-colour microarray design
    MACALCULATE corrects and transforms two-colour microarray differential expressions
    MNORMALIZE normalizes two-colour microarray data
    MAESTIMATE estimates treatment effects from a two-colour microarray design
    AFFYMETRIX estimates expression values for Affymetrix slides.
    MABGCORRECT performs background correction of Affymetrix slides
    MAROBUSTMEANS does a robust means analysis for Affymetrix slides
    MARMA calculates Affymetrix expression values
    MAVDIFFERENCE applies the average difference algorithm to Affymetrix data
    DMADENSITY plots the empirical CDF or PDF (kernel smoothed) by groups
    MAHISTOGRAM plots histograms of microarray data
    MAPLOT produces two-dimensional plots of microarray data
    MAANOVA does analysis of variance of single-channel microarray data
    MAREGRESSION does regressions for single-channel microarray data
    MASHADE produces shade plots to display spatial variation of microarray data
    MAVOLCANO produces volcano plots of microarray data
    MAPCLUSTER clusters probes or genes with microarray data
    MASCLUSTER clusters microarray slides
    MA2CLUSTER performs a two-way clustering of microarray data by probes (or genes) and slides
    FDRBONFERRONI estimates false discovery rates by a Bonferroni-type procedure
    FDRMIXTURE estimates false discovery rates using mixture distributions
    MAEBAYES modifies t-values by an empirical Bayes method.
    MPOLISH performs a median polish of two-way data
    QNORMALIZE performs quantile normalization
    THINPLATE calculates the basis functions for thin-plate splines
    TUKEYBIWEIGHT estimates means using the Tukey biweight algorithm
Updated on May 20, 2019

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